RNA polymerases B and C are more closely related to each other than to RNA polymerase A

Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation

TATA-box binding protein (TBP) is required for every single transcription event in archaea and eukaryotes. It binds DNA and harbors two repeats with an internal structural symmetry that show sequence asymmetry. At various times in evolution, TBP has acquired multiple interaction partners and different organisms have evolved TBP paralogs with additional protein regions. Together, these observations raise questions of what molecular determinants (i.e. key residues) led to the ability of TBP to acquire new interactions, resulting in an increasingly complex transcriptional system in eukaryotes. We present a comprehensive study of the evolutionary history of TBP and its interaction partners across all domains of life, including viruses. Our analysis reveals the molecular determinants and suggests a unified and multi-stage evolutionary model for the functional innovations of TBP. These findings highlight how concerted chemical changes on a conserved structural scaffold allow for the emergence of complexity in a fundamental biological process.

The TATA-box binding protein (TBP) is required for transcription initiation in archaea and eukaryotes. Here the authors delineate how TBP’s function has evolved new functional features through context-dependent interactions with various protein partners.

Odd RNA polymerases or the A(B)C of eukaryotic transcription

Pioneering studies on eukaryotic transcription were undertaken with the bacterial system in mind. Will the bacterial paradigm apply to eukaryotes? Are there promoter sites scattered in the eukaryotic genome, and sigma-like proteins? Why three forms of RNA polymerase in eukaryotic cells? Why are they structurally so complex, in particular RNA polymerases I and III, compared to the bacterial enzyme? These questions and others that were raised along the way are evoked in this short historical survey of odd RNA polymerases studies, with some emphasis on the contribution of these studies to our global understanding of eukaryotic transcription systems. This article is part of a Special Issue entitled: Transcription by Odd Pols.

TFIIB-related factors in RNA polymerase I transcription

Eukaryotic RNA polymerases (Pol) I, II, III and archaeal Pol use a related set of general transcription factors to recognize promoter sequences and recruit Pol to promoters and to function at key points in the transcription initiation mechanism. The TFIIB-like general transcription factors (GTFs) function during several important and conserved steps in the initiation pathway for Pols II, III, and archaeal Pol. Until recently, the mechanism of Pol I initiation seemed unique, since it appeared to lack a GTF paralogous to the TFIIB-like proteins. The surprising recent discovery of TFIIB-related Pol I general factors in yeast and humans highlights the evolutionary conservation of transcription initiation mechanisms for all eukaryotic and archaeal Pols. These findings reveal new roles for the function of the Pol I GTFs and insight into the function of TFIIB-related factors. Models for Pol I transcription initiation are reexamined in light of these recent findings. This article is part of a Special Issue entitled: Transcription by Odd Pols.

Characterization of the interactions of mammalian RNA polymerase I associated proteins PAF53 and PAF49

Masami Muramatsu's laboratory demonstrated the critical role of RNA polymerase I (Pol I)-associated factor PAF53 in mammalian rRNA transcription. They have also identified a second polymerase associated factor, PAF49. Both PAF49 and PAF53 copurify with that fraction of the RNA polymerase I molecules that can function in transcription initiation in vitro. PAF49 and PAF53 are the mammalian homologues of two subunits of yeast RNA polymerase I, A34.5 and A49, that form a TFIIF-related subcomplex in yeast RNA polymerase I. In light of those publications, we investigated the interactions between various deletion and substitution mutants of mammalian PAF49 and PAF53 with the purpose of identifying those domains of the mammalian proteins that interact. Comparison of our results with structural studies on yeast A34.5 and A49 demonstrates that the yeast and mammalian proteins may in fact share structural similarities. In fact, the deletion mutagenesis data confirmed and extended the structural studies. For example, amino acids 41-86 of PAF49 were sufficient to provide the basis for heterodimerization. In silico structural analysis predicted that this region could assume a structure similar to the homologous region of yeast A34.5. Those similarities are insufficient, by themselves, for the proteins to form interspecific heterodimers. However, substitution of amino acids 52-98 of yeast A34.5 with amino acids 41-86 of mammalian PAF49 resulted in a protein that could heterodimerize with mouse PAF53.

A multistep process gave rise to RNA polymerase IV of land plants

Since their discovery in Metazoa, the three nuclear RNA polymerases (RNAPs) have been found in fungi, plants, and diverse protists. In all eukaryotes studied to date, RNAPs I, II, and III collectively transcribe all major RNAs made in the nucleus. We have found genes for the largest subunit (RPD1/RPE1) of a new DNA-dependent RNAP, RNAP IV, in all major land plant taxa and in closely related green algae. Genes for the second-largest subunit (RPD2) of this enzyme were found in all land plants. Phylogenetic study indicates that RNAP IV genes are sister to the corresponding RNAP II genes. Our results show the genesis of RNAP IV to be a multistep process in which the largest and second-largest subunit genes evolved by independent duplication events in the ancestors of Charales and land plants. These findings provide insights into evolutionary mechanisms that can explain the origin of multiple RNAPs in the eukaryotic nucleus.

Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia

The Giardia lamblia genome sequencing project affords us a unique opportunity to conduct comparative analyses of core cellular systems between early and late-diverging eukaryotes on a genome-wide scale. We report a survey to identify canonical transcription components in Giardia, focusing on RNA polymerase (RNAP) subunits and transcription-initiation factors. Our survey revealed that Giardia contains homologs to 21 of the 28 polypeptides comprising eukaryal RNAPI, RNAPII, and RNAPIII; six of the seven RNAP subunits without giardial homologs are polymerase specific. Components of only four of the 12 general transcription initiation factors have giardial homologs. Surprisingly, giardial TATA-binding protein (TBP) is highly divergent with respect to archaeal and higher eukaryotic TBPs, and a giardial homolog of transcription factor IIB was not identified. We conclude that Giardia represents a transition during the evolution of eukaryal transcription systems, exhibiting a relatively complete set of RNAP subunits and a rudimentary basal initiation apparatus for each transcription system. Most class-specific RNAP subunits and basal initiation factors appear to have evolved after the divergence of Giardia from the main eukaryotic line of descent. Consequently, Giardia is predicted to be unique in many aspects of transcription initiation with respect to paradigms derived from studies in crown eukaryotes.

The Leishmania major RNA polymerase II largest subunit lacks a carboxy-terminus heptad repeat structure and its encoding gene is linked with the calreticulin gene

The gene encoding the RNA polymerase II largest subunit (RPOIILS) has been isolated and sequenced from the kinetoplastid protozoan, Leishmania (Leishmania) major. The RPOIILS gene was shown to be present as a single copy and is composed of an uninterrupted open reading frame of 4.99 kb, specifying a protein 1663 aa in length with a predicted molecular mass of approximately 185 kDa. The carboxy terminus domain (CTD) of the RPOIILS from L. (L.) major, typical of the more evolutionary primitive protozoa, lacked a heptad repeat structure which is present in higher eukaryotes and some other protozoan phyla. Comparison of the predicted aa composition of the CTD from a diverse range of eukaryotic species revealed the abundance of Ser and Pro residues as the only discernible evolutionary conservative feature. A putative ATG start codon for an additional expressed sequence was located 1.1 kb downstream of the L. (L.) major RPOIILS gene stop codon. Nucleic acid database searches revealed the identity of this gene as that encoding the calcium binding protein calreticulin (CLT). The close proximity of the RPOIILS and CLT genes in L. (L.) major raises the possibility that these genes are transcribed as part of the same polycistronic unit.

Isolation and characterization of monoclonal antibodies directed against subunits of human RNA polymerases I, II, and III

Human nuclei contain three different RNA polymerases: polymerases I, II, and III. Each polymerase is a multi-subunit enzyme with 12-17 subunits. The localization of these subunits is limited by the paucity of antibodies suitable for immunofluorescence. We now describe eight different monoclonal antibodies that react specifically with RPB6 (also known as RPA20, RPB14.4, or RPC20), RPB8 (RPA18, RPB17, or RPC18), RPC32, or RPC39 and which are suitable for such studies. Each antibody detects one specific band in immunoblots of nuclear extracts; each also immunoprecipitates large complexes containing many other subunits. When used for immunofluorescence, antibodies against the subunits shared by all three polymerases (i.e., RPB6, RPB8) gave a few bright foci in nucleoli and nucleoplasm, as well as many fainter nucleoplasmic foci; all the bright foci were generally distinct from speckles containing Sm antigen. Antibodies against the two subunits found only in polymerase III (i.e., RPC32, RPC39) gave a few bright and many faint nucleoplasmic foci, but no nucleolar foci. Growth in two transcriptional inhibitors-5, 6-dichloro-1-beta-d-ribofuranosylbenzimidazole and actinomycin D-led to the redistribution of each subunit in a characteristic manner.

The largest subunit of human RNA polymerase III is closely related to the largest subunit of yeast and trypanosome RNA polymerase III

In both yeast and mammalian systems, considerable progress has been made toward the characterization of the transcription factors required for transcription by RNA polymerase III. However, whereas in yeast all of the RNA polymerase III subunits have been cloned, relatively little is known about the enzyme itself in higher eukaryotes. For example, no higher eukaryotic sequence corresponding to the largest RNA polymerase III subunit is available. Here we describe the isolation of cDNAs that encode the largest subunit of human RNA polymerase III, as suggested by the observations that (1) antibodies directed against the cloned protein immunoprecipitate an active enzyme whose sensitivity to different concentrations of alpha-amanitin is that expected for human RNA polymerase III; and (2) depletion of transcription extracts with the same antibodies results in inhibition of transcription from an RNA polymerase III, but not from an RNA polymerase II, promoter. Sequence comparisons reveal that regions conserved in the RNA polymerase I, II, and III largest subunits characterized so far are also conserved in the human RNA polymerase III sequence, and thus probably perform similar functions for the human RNA polymerase III enzyme.

Three human RNA polymerase III-specific subunits form a subcomplex with a selective function in specific transcription initiation

Transcription by RNA polymerase III involves recruitment of the polymerase by template-bound accessory factors, followed by initiation, elongation, and termination steps. An immunopurification approach has been used to demonstrate that human RNA Pol III is composed of 16 subunits, some of which are apparently modified in HeLa cells. Partial denaturing conditions and sucrose gradient sedimentation at high salt result in the dissociation of a subcomplex that includes hRPC32, hRPC39, and hRPC62. Cognate cDNAs were isolated and shown to encode three subunits that are specific to RNA Pol III and homologous to three yeast subunits. The human RNA Pol III core lacking the subcomplex functions in transcription elongation and termination following nonspecific initiation on a tailed template, but fails to show promoter-dependent transcription initiation in conjunction with accessory factors. The capability for specific transcription initiation can be restored either by the natural subcomplex or by a stable subcomplex composed of recombinant hRPC32, hRPC39, and hRPC62 polypeptides. One component (hRPC39) of this subcomplex interacts physically with both hTBP and hTFIIIB90, two subunits of human RNA Pol III transcription initiation factor IIIB. These data strongly suggest that the hRPC32-hRPC39-hRPC62 subcomplex directs RNA Pol III binding to the TFIIIB-DNA complex via the interactions between TFIIIB and hRPC39.

Identification of previously unrecognized common elements in eukaryotic promoters. A ribosomal RNA gene initiator element for RNA polymerase I

A new ribosomal RNA promoter element with a functional role similar to the RNA polymerase II initiator (Inr) was identified. This sequence, which we dub the ribosomal Inr (rInr) is unusually conserved, even in normally divergent RNA polymerase I promoters. It functions in the recruitment of the fundamental, TATA-binding protein (TBP)-containing transcription factor, TIF-IB. All upstream elements of the exceptionally strong Acanthamoeba castellanii ribosomal RNA core promoter, to within 6 base pairs of the transcription initiation site (tis), can be deleted without loss of specific transcription initiation. Thus, the A. castellanii promoter can function in a manner similar to RNA polymerase II TATA-less promoters. Sequence-specific photo-cross-linking localizes a 96-kDa subunit of TIF-IB and the second largest RNA polymerase I subunit (A133) to the rInr sequence. A185 also photo-cross-links when polymerase is stalled at +7.

Transcription of the human T-cell lymphotropic virus type I promoter by an alpha-amanitin-resistant polymerase

The human T-lymphotropic virus type I (HTLV-I) promoter contains the structural features of a typical RNA polymerase II (pol II) template. The promoter contains a TATA box 30 bp upstream of the transcription initiation site and binding sites for several pol II transcription factors, and long poly(A)+ RNA is synthesized from the integrated HTLV-I proviral DNA in vivo. Consistent with these characteristics, HTLV-I transcription activity was reconstituted in vitro by using TATA-binding protein, TFIIA, recombinant TFIIB, TFIIE, and TFIIF, TFIIH, and pol II. Transcription of the HTLV-I promoter in the reconstituted system requires RNA pol II. In HeLa whole cell extracts, however, the HTLV-I long terminal repeat also contains an overlapping transcription unit (OTU). HTLV-I OTU transcription is initiated at the same nucleotide site as the RNA isolated from the HTLV-I-infected cell line MT-2 but was not inhibited by the presence of alpha-amanitin at concentrations which inhibited the adenovirus major late pol II promoter (6 micrograms/ml). HTLV-I transcription was inhibited when higher concentrations of alpha-amanitin (60 micrograms/ml) were used, in the range of a typical pol III promoter (VA-I). Neutralization and depletion experiments with three distinct pol II antibodies demonstrate that RNA pol II is not required for HTLV-I OTU transcription. Antibodies to basal transcription factors TATA-binding protein and TFIIB, but not TFIIIC, inhibited HTLV-I OTU transcription. These observations suggest that the HTLV-I long terminal repeat contains overlapping promoters, a typical pol II promoter and a unique pol III promoter which requires a distinct set of transcription factors.

Human RNA polymerase II subunit hRPB14 is homologous to yeast RNA polymerase I, II, and III subunits (AC19 and RPB11) and is similar to a portion of the bacterial RNA polymerase alpha subunit

The cDNA cloning of the human polII 14-kDa subunit, hRPB14, and the comparison of its aa sequence with those of other pol subunits are described. The aa sequence of hRPB14 has homology to yeast poIII subunit RPB11 (44%), to a common subunit of yeast polI and polIII AC19 (24%) and to a Caenorhabditis elegans sequence (33%). hRPB14 contains a 19-aa motif, located in its N terminus, which was also found in human polII 33-kDa subunit hRPB33, yeast pol subunits (AC40, AC19, RPB3 and RPB11), and in the bacterial pol alpha subunit, which was involved in subunit assembly. This motif was also conserved in the conjugation-specific gene products of Tetrahymena (CnjC), Merchantia polymorpha chloroplast DNA (RNLVA) and C. elegans DNA (CEF58A4; deduced from the nucleotide sequence and of unknown function). The evolutionary emergence of a probable eukaryotic heterodimer, hRPB14/hRPB33, from a prokaryotic homodimer, alpha 2, is hypothesized.

Immunocytochemical characterization of human NOR-90 (upstream binding factor) and associated antigens reactive with autoimmune sera. Two MR forms of NOR-90/hUBF autoantigens

The 90-kDa nucleolus organizer region autoantigen (NOR-90) was previously shown to be identical to the human upstream binding factor (hUBF) and composed of two Mr forms. In this study, thirteen human anti-NOR-90/hUBF autoimmune sera were used to further characterize NOR-90/hUBF and its associated autoantigens. Nucleolar and nucleoplasmic staining of interphase cells and NOR staining in mitosis were observed with all sera by immunofluorescence. All sera showed equal reactivity with both high and low Mr forms in Western blotting and immunoprecipitation, suggesting that the cellular content and distribution for both Mr forms were approximately equal. Using extracts of [35S]methionine- and [32P]orthophosphate-labeled cells, phosphorylated and nonphosphorylated NOR-90/hUBF were identified for both Mr forms and these two populations were recognized by human autoantibodies. In immunoprecipitation analyses, the nonphosphorylated population was readily extracted while the phosphorylated population was tightly bound. Clinical data were available for 8 patients in whom anti-NOR-90/hUBF autoantibodies were present. They had diverse diagnoses including SLE, rheumatoid arthritis and malignancies. Although only one patient was diagnosed as scleroderma, Raynaud's phenomenon was observed in 4 of the 8 patients. Interestingly, one NOR-90/hUBF serum was shown to contain additional antibodies to RNA polymerases I and II.

The TATA-binding protein is required for transcription by all three nuclear RNA polymerases in yeast cells

Using temperature- and proteolytically sensitive derivatives to inactivate the function of the yeast TATA-binding protein (TBP) in vivo, we investigated the requirement of TBP for transcription by the three nuclear RNA polymerases in yeast cells. TBP is required for RNA polymerase II (pol II) transcription from promoters containing conventional TATA elements as well as functionally distinct promoters that lack TATA-like sequences. TBP is also required for transcription of the U6 snRNA and two different tRNA genes mediated by RNA pol III as well as transcription of ribosomal RNA mediated by RNA pol I. For all promoters tested, transcription decreases rapidly and specifically upon inactivation of TBP, strongly suggesting that TBP is directly involved in the transcription process. These observations suggest that TBP is required for transcription of all nuclearly encoded genes in yeast, although distinct molecular mechanisms are probably involved for the three RNA polymerase transcription machineries.

The C-terminal domain of RNA polymerase II of the malaria parasite Plasmodium berghei

The C-terminal domain (CTD) of RNA polymerase II (RNAP) has an essential function in the regulation of transcription. The CTD of the human malaria parasite, Plasmodium falciparum, differs dramatically from that of higher eukaryotes. To determine whether this is a general feature of malarial parasites, we have analysed the CTD of the distantly related rodent malaria parasite P.berghei. The CTDs of the two parasites enzymes are very similar in amino acid composition and contain the basic structure of most eukaryotic CTDs, which is a tandem repeat of a heptapeptide (SPTSPSY). The CTD of P.berghei differs, however, in three aspects from the CTD of P.falciparum and other eukaryotes. First, both domains show a divergence from the consensus sequence at position 6 of the heptapeptide repeat. The Ser6 is always substituted, with a bias for lysine. The latter substitution might increase the binding efficiency to the DNA template. Second, the rodent and human malarial CTDs contain a 3' extension of, respectively, 66 or 67 amino acid residues. This tail-piece is unique among eukaryotes. Third, the enlargement of the CTD of the human parasite by six heptapeptide repeats is most likely generated by a recent amplification of a specific repeat unit.

RNA polymerase III (C) and its transcription factors

Transcription of small genes by RNA polymerase III or C (pol III) involves many of the strategies that are used for transcription complex formation and occasionally the same components as those used by RNA polymerase II or B (pol II). Transcription complex formation is a multistep process that leads to the binding of a single initiation factor, TFIIIB, which in turn directs the selection of pol III. The general transcription factor TFIID can be involved in both pol II and pol III transcription. These and other similarities point towards a unifying mechanism for eukaryotic transcription initiation.

Identification of the genes coding for the second-largest subunits of RNA polymerases I and III of Drosophila melanogaster

We have isolated cDNA and genomic clones of Drosophila melanogaster by cross-hybridization with a 658 bp fragment of the yeast gene coding for the second-largest subunit of RNA polymerase III (RET1). Determination of the sequence by comparison of genomic and cDNA regions reveals an ORF of 3405 nucleotides which is interrupted in the genomic sequence by an intron of 48 bp. The deduced polypeptide consists of 1135 amino acids with a calculated molecular weight of 128 kDa. The protein sequence shows the same conserved regions of homology as those observed for all the second-largest subunits of RNA polymerases cloned so far. The gene (DmRP128) obviously codes for a second-largest subunit of an RNA polymerase which is different from DmRP140 and DmRP135. We have purified three distinct RNA polymerase activities from D. melanogaster. By using specific RNA polymerase inhibitors in enzyme assays and by comparing their subunit composition we were able to distinguish between RNA polymerase I, II, and III. RNA polymerase preparations of D. melanogaster were blotted and the second-largest subunits were identified with antibodies raised against polypeptides expressed from DmRP128 and DmRP135. Anti-DmRP135 antibodies react strongly with the second-largest subunit of RNA polymerase I but do not react with the respective subunits of RNA polymerase II and III. The second-largest subunit of RNA polymerase III is only recognized by anti-DmRP128. Previously, we have claimed that DmRP135 codes for the second-largest subunit of RNA polymerase III.(ABSTRACT TRUNCATED AT 250 WORDS)

The cloned RNA polymerase II transcription factor IID selects RNA polymerase III to transcribe the human U6 gene in vitro

Although the human U2 and U6 snRNA genes are transcribed by different RNA polymerases (i.e., RNA polymerases II and III, respectively), their promoters are very similar in structure. Both contain a proximal sequence element (PSE) and an octamer motif-containing enhancer, and these elements are interchangeable between the two promoters. The RNA polymerase III specificity of the U6 promoter is conferred by a single A/T-rich element located around position -25. Mutation of the A/T-rich region converts the U6 promoter into an RNA polymerase II promoter, whereas insertion of the A/T-rich region into the U2 promoter converts that promoter into an RNA polymerase III promoter. We show that this A/T-rich element can be replaced by a number of TATA boxes derived from mRNA promoters transcribed by RNA polymerase II with little effect on RNA polymerase III transcription. Furthermore, the cloned RNA polymerase II transcription factor TFIID both binds to the U6 A/T-rich region and directs accurate RNA polymerase III transcription in vitro. Mutations in the U6 A/T-rich region that convert the U6 promoter into an RNA polymerase II promoter also abolish TFIID binding. Together, these observations suggest that in the human snRNA promoters, unlike in mRNA promoters, binding of TFIID directs the assembly of RNA polymerase III transcription complexes, whereas the lack of TFIID binding results in the assembly of RNA polymerase II snRNA transcription complexes.

RNA polymerase III transcription

Remarkable progress has been made in defining the functional significance of the protein-DNA interactions involved in transcription complex formation on yeast tRNA and 5S RNA genes. This new information leads to a re-evaluation of how the class III gene transcription machinery operates.

Alteration of the RNA polymerase specificity of U3 snRNA genes during evolution and in vitro

We present evidence that the genes encoding U3 snRNA in plants are transcribed by RNA polymerase III (pol III) and not by RNA polymerase II (pol II) as in vertebrates or lower eukaryotes. The U3 gene is the only known example of a gene transcribed by different polymerases in different organisms. It is possible to convert the plant U3 gene into a functional pol II-transcribed gene by manipulating the spacing between the promoter elements and inserting a pol II-specific termination signal. Pol II-transcribed U3 RNA, containing the 5'-terminal cap different from that present in the wild-type counterpart, is packaged in transfected protoplasts into U3 snRNP precipitable with anti-fibrillarin antibodies. These findings provide further evidence for the common ancestry of the pol II and pol III transcription systems, and indicate that promoter diversification in some genes has occurred relatively recently.

Characterization of the RNA polymerases of Crithidia fasciculata

We have characterized the crithidial RNA polymerases (RNAPs). The RNAPs from this organism were resolved by chromatography and could be classified into RNAP I, II and III because of their differential sensitivity to class-specific RNA polymerase inhibitors, such as alpha-amanitin (ama) and tagetitoxin. The three RNAP classes were subsequently characterized in nuclear run-ons using class-specific DNA templates and the inhibitory effect of ama on RNA chain elongation. These experiments showed that Crithidia fasciculata contains the normal set of eukaryotic RNAPs. However, RNAP II was found to be relatively resistant to ama, which seems to be a general feature of kinetoplastid parasites. Tagetitoxin, a potent inhibitor of purified crithidial RNAP III, does not inhibit RNAP III in nuclear run-on experiments, suggesting that the inhibitory effect of tagetitoxin depends on the enzyme conformation, i.e. 'naked' enzyme versus that in a transcription complex. Finally, the role of RNAP III in the transcription of the mini-exon genes, which provide the 5' end of each mRNA, is discussed.

Participation of the TATA factor in transcription of the yeast U6 gene by RNA polymerase C

Fractionation of transcription extracts has led to the identification of multiple transcription factors specific for each form of nuclear RNA polymerase. Accurate transcription in vitro of the yeast U6 RNA gene by RNA polymerase C requires at least two factors. One of them was physically and functionally indistinguishable from transcription factor IID (TFIID or BTF1), a pivotal component of polymerase B transcription complexes, which binds to the TATA element. Purified yeast TFIID (yIID) or bacterial extracts that contained recombinant yIID were equally competent to direct specific transcription of the U6 gene by RNA polymerase C. The results suggest the formation of a hybrid transcription machinery, which may imply an evolutionary relation between class B and class C transcription factors.

Common RNA polymerase I, II, and III upstream elements in mouse 7SK gene locus revealed by the inverse polymerase chain reaction

7SK RNA in mammalian cells is derived from a gene or genes belonging to a middle-repetitive family in the genome. Standard library search techniques applied to isolating such genes are complicated by the finding of multiple truncated or otherwise modified versions of the sequence, whereas the true gene loci can sometimes be eliminated from amplified libraries. After an unsuccessful search for the 7SK RNA gene in four mouse genomic libraries, we used the inverse polymerase chain reaction (IPCR) on fractionated genomic DNA to characterize sequences containing complete copies of 7SK plus flanking regions for analysis of putative transcription regulatory sequences. Direct sequence of IPCR-amplified material allowed for selection of upstream and downstream primers which could then be used for direct PCR, sequencing, and characterization of the mouse 7SK gene locus. So far, we found only one complete copy of the canonical 7SK gene that differed from the human sequence in only 4 bases. The gene is flanked by a very well-conserved upstream control region that includes a TATA motif, two direct repeats, and a proximal sequence element common to mammalian genes transcribed by all three RNA polymerases. The 3' region contains multiple stretches of T residues, typical of class III terminators.

Phylogenetic analysis of the RNA polymerases of Trypanosoma brucei, with special reference to class-specific transcription

We have sequenced the genes encoding to largest subunits of the three classes of DNA-dependent RNA polymerases of Trypanosoma brucei. The nucleotide and deduced amino acid sequences were compared and aligned with the corresponding sequences of other eukaryotes. Phylogenetic relationships were subsequently calculated with a distant matrix, a bootstrapped parsimony and a maximum-likelihood method. These independent calculations resulted in trees with very similar topologies. The analyses show that all the largest subunits of T. brucei are evolutionarily distant members within each of the three RNA polymerase classes. An early separation of the trypanosomal subunits from the eukaryotic lineage might form the fundamental basis for the unusual transcription process of this species. Finally, all dendrograms show a separate ramification for the largest subunit of RNA polymerase I, II and III. RNA polymerase II and/or III form a bifurcation with the archaebacterial lineage, RNA polymerase I, however, arises separately from the eubacterial beta' lineage. This suggests that the three eukaryotic RNA polymerase classes are not simply derived by two gene duplications of an ancestral gene with subsequent differentiation.

Structural study of the yeast RNA polymerase A. Electron microscopy of lipid-bound molecules and two-dimensional crystals

Two-dimensional crystals of yeast RNA polymerase A (I) were obtained by interaction with positively charged lipid layers. The analysis of single molecular images of lipid-bound RNA polymerases showed that the enzyme was preferentially oriented by the lipid phase, which probably facilitated crystallization. Electron micrographs of the crystals revealed a rectangular unit cell 25.8 nm by 45.6 nm in size containing four RNA polymerase dimers related by P22(1)2(1) symmetry. The projection map showed, at about 2.5 nm resolution, two different views of the enzyme characterized by two bent arms, which appeared to cross at one end. These arms are likely to contain the A190 and A135 subunits and delimit a 3 to 4 nm wide groove. Additional structural features were observed and compared to the Escherichia coli enzyme.

Unraveling the complexities of transcription by RNA polymerase III

The biosynthesis of proteins and nucleic acids in eukaryotes requires the participation of numerous small RNAs, many of which are products of RNA polymerase III transcription. How cells are able to coordinate the synthesis of these RNAs during growth and replication has been the subject of recent exciting and thought-provoking studies. We review the progress in this area, and focus upon shared properties between transcription systems having different functions.

RNA-polymerase specificity of transcription of Arabidopsis U snRNA genes determined by promoter element spacing

Although most eukaryotic genes known to be transcribed by RNA polymerase III have intragenic promoter elements, some are similar to genes transcribed by RNA polymerase II in that they have upstream promoters (reviewed in refs 1-4). Transcription of the vertebrate U6 and 7SK RNA genes by RNA polymerase III depends exclusively upon upstream signals, some of which are indistinguishable from the elements essential for polymerase II-specific genes. In the plant Arabidopsis thaliana the promoter elements for the U6 and U2 small nuclear RNA genes, transcribed by RNA polymerases III and II respectively, are identical, comprising a -30 TATA box and an upstream element specific for small nuclear RNA genes. The distance between these elements differs, however. Here we report evidence that this separation is crucial in determining whether the genes are transcribed by polymerase II or III.

Electron microscopic study of yeast RNA polymerase A: analysis of single molecular images

The structural features of the yeast DNA-dependent RNA polymerase A (I) were examined by Scanning Transmission Electron Microscopy. The enzyme was absorbed in its monomeric form and negatively stained prior to digital image acquisition at low dose. The signal to noise ratio of single particle images was improved through averaging of a large number of previously aligned and partitioned images. Six classes of images were obtained reproducibly which corresponded to different projections of the enzyme. The enzyme structure was characterized by its presence of two curved arms which defined a longitudinal cleft. By analogy with the Escherichia coli enzyme, these arms could correspond to the two large subunits A135 and A190.

Subunits shared by eukaryotic nuclear RNA polymerases

RNA polymerases I, II, and III share three subunits that are immunologically and biochemically indistinguishable. The Saccharomyces cerevisiae genes that encode these subunits (RPB5, RPB6, and RPB8) were isolated and sequenced, and their transcriptional start sites were deduced. RPB5 encodes a 25-kD protein, RPB6, an 18-kD protein, and RPB8, a 16-kD protein. These genes are single copy, reside on different chromosomes, and are essential for viability. The fact that the genes are single copy, corroborates previous evidence suggesting that each of the common subunits is identical in RNA polymerases I, II, and III. Furthermore, immunoprecipitation of RPB6 coprecipitates proteins whose sizes are consistent with RNA polymerase I, II, and III subunits. Sequence similarity between the yeast RPB5 protein and a previously characterized human RNA polymerase subunit demonstrates that the common subunits of the nuclear RNA polymerases are well conserved among eukaryotes. The presence of these conserved and essential subunits in all three nuclear RNA polymerases and the absence of recognizable sequence motifs for DNA and nucleoside triphosphate-binding indicate that the common subunits do not have a catalytic role but are important for a function shared by the RNA polymerases such as transcriptional efficiency, nuclear localization, enzyme stability, or coordinate regulation of rRNA, mRNA, and tRNA synthesis.

Cloning and sequence determination of the gene encoding the largest subunit of the fission yeast Schizosaccharomyces pombe RNA polymerase I

The gene encoding the largest subunit of RNA polymerase I (SPRPA190) was cloned from the fission yeast Schizosaccharomyces pombe by cross-hybridization with a probe containing part of the corresponding Saccharomyces cerevisiae gene RPA190. The SPRPA190 gene is present in a single copy per haploid genome and is essential for cell growth. The polypeptide encoded by this gene, as deduced from the nucleotide sequence of the uninterrupted coding frame, consists of 1689 amino acids and its calculated Mr is 189,300. The amino acid identity between the subunits of the two yeast species is 50%. Amino acid sequence conservation covers the regions previously suggested to be functionally important for the S. cerevisiae enzyme. In addition, two markedly hydrophilic regions recognized in the S. cerevisiae polypeptide can also be recognized in the S. pombe polypeptide in approximately the same positions, even though the amino acid sequences in these regions are diverged from each other. In the 5'-flanking region of the gene, several nucleotide sequence elements are detected which are also found in the two S. pombe ribosomal protein genes so far sequenced.